Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.

Structural Basis for Virulence Activation of Francisella tularensis.

The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with the σ70-associated RNAP holoenzyme (RNAPσ70), forming a virulence-specialized polymerase. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence, but the mechanism is unknown. Here we report FtRNAPσ70-promoter-DNA, FtRNAPσ70-(MglA-SspA)-promoter DNA, and FtRNAPσ70-(MglA-SspA)-ppGpp-PigR-promoter DNA cryo-EM structures. Structural and genetic analyses show MglA-SspA facilitates σ70 binding to DNA to regulate virulence and virulence-enhancing genes. Our Escherichia coli RNAPσ70-homodimeric EcSspA structure suggests this is a general SspA-transcription regulation mechanism. Strikingly, our FtRNAPσ70-(MglA-SspA)-ppGpp-PigR-DNA structure reveals ppGpp binding to MglA-SspA tethers PigR to promoters. PigR in turn recruits FtRNAP αCTDs to DNA UP elements. Thus, these studies unveil a unique mechanism for Ft pathogenesis involving a virulence-specialized RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes.

Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen Cryptococcus neoformans: A target for antifungals.

Invasive fungal diseases are a major threat to human health, resulting in more than 1.5 million annual deaths worldwide. The arsenal of antifungal therapeutics remains limited and is in dire need of drugs that target additional biosynthetic pathways that are absent from humans. One such pathway involves the biosynthesis of trehalose. Trehalose is a disaccharide that is required for pathogenic fungi to survive in their human hosts. In the first step of trehalose biosynthesis, trehalose-6-phosphate synthase (Tps1) converts UDP-glucose and glucose-6-phosphate to trehalose-6-phosphate. Here, we report the structures of full-length Cryptococcus neoformans Tps1 (CnTps1) in unliganded form and in complex with uridine diphosphate and glucose-6-phosphate. Comparison of these two structures reveals significant movement toward the catalytic pocket by the N terminus upon ligand binding and identifies residues required for substrate binding, as well as residues that stabilize the tetramer. Intriguingly, an intrinsically disordered domain (IDD), which is conserved among Cryptococcal species and closely related basidiomycetes, extends from each subunit of the tetramer into the "solvent" but is not visible in density maps. We determined that the IDD is not required for C. neoformans Tps1-dependent thermotolerance and osmotic stress survival. Studies with UDP-galactose highlight the exquisite substrate specificity of CnTps1. In toto, these studies expand our knowledge of trehalose biosynthesis in Cryptococcus and highlight the potential of developing antifungal therapeutics that disrupt the synthesis of this disaccharide or the formation of a functional tetramer and the use of cryo-EM in the structural characterization of CnTps1-ligand/drug complexes.

Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase.

Levels of the cellular dNTPs, the direct precursors for DNA synthesis, are important for DNA replication fidelity, cell cycle control, and resistance against viruses. Escherichia coli encodes a dGTPase (2'-deoxyguanosine-5'-triphosphate [dGTP] triphosphohydrolase [dGTPase]; dgt gene, Dgt) that establishes the normal dGTP level required for accurate DNA replication but also plays a role in protecting E. coli against bacteriophage T7 infection by limiting the dGTP required for viral DNA replication. T7 counteracts Dgt using an inhibitor, the gene 1.2 product (Gp1.2). This interaction is a useful model system for studying the ongoing evolutionary virus/host "arms race." We determined the structure of Gp1.2 by NMR spectroscopy and solved high-resolution cryo-electron microscopy structures of the Dgt-Gp1.2 complex also including either dGTP substrate or GTP coinhibitor bound in the active site. These structures reveal the mechanism by which Gp1.2 inhibits Dgt and indicate that Gp1.2 preferentially binds the GTP-bound form of Dgt. Biochemical assays reveal that the two inhibitors use different modes of inhibition and bind to Dgt in combination to yield enhanced inhibition. We thus propose an in vivo inhibition model wherein the Dgt-Gp1.2 complex equilibrates with GTP to fully inactivate Dgt, limiting dGTP hydrolysis and preserving the dGTP pool for viral DNA replication.

Ion channel chameleons: Switching ion selectivity by alternative splicing.

Voltage-gated sodium and calcium channels are distinct, evolutionarily related ion channels that achieve remarkable ion selectivity despite sharing an overall similar structure. Classical studies have shown that ion selectivity is determined by specific binding of ions to the channel pore, enabled by signature amino acid sequences within the selectivity filter (SF). By studying ancestral channels in the pond snail (Lymnaea stagnalis), Guan et al. showed in a recent JBC article that this well-established mechanism can be tuned by alternative splicing, allowing a single CaV3 gene to encode both a Ca2+-permeable and an Na+-permeable channel depending on the cellular context. These findings shed light on mechanisms that tune ion selectivity in physiology and on the evolutionary basis of ion selectivity.

Molecular Probing of the Microscopic Pressure at Contact Interfaces.

Obtaining insights into friction at the nanoscopic level and being able to translate these into macroscopic friction behavior in real-world systems is of paramount importance in many contexts, ranging from transportation to high-precision technology and seismology. Since friction is controlled by the local pressure at the contact it is important to be able to detect both the real contact area and the nanoscopic local pressure distribution simultaneously. In this paper, we present a method that uses planarizable molecular probes in combination with fluorescence microscopy to achieve this goal. These probes, inherently twisted in their ground states, undergo planarization under the influence of pressure, leading to bathochromic and hyperchromic shifts of their UV-vis absorption band. This allows us to map the local pressure in mechanical contact from fluorescence by exciting the emission in the long-wavelength region of the absorption band. We demonstrate a linear relationship between fluorescence intensity and (simulated) pressure at the submicron scale. This relationship enables us to experimentally depict the pressure distribution in multiasperity contacts. The method presented here offers a new way of bridging friction studies of the nanoscale model systems and practical situations for which surface roughness plays a crucial role.

Optimal reimplantation timing in two-stage exchange for periprosthetic joint infection: an observative cohort study in Asian population.

BACKGROUND: The optimal timing for reimplantation for periprosthetic joint infection (PJI) has not been established and varies from a few weeks to several months. The aim of this study was to assess the commendable time between implant removal and reimplantation in patients who underwent two-stage exchange arthroplasty for PJI. METHODS: We retrospectively reviewed 361 patients who were treated with two-stage exchange arthroplasty for hip and knee chronic PJI at our institution between January 2000 and December 2018. Patient characteristics, comorbidities, surgical variables, microbiology data, and time to reimplantation were recorded. All patients were followed for a minimum of one year. Treatment failure was defined by Delphi criteria. Logistic regression analyses were used to calculate survival rates and adjusted odds ratios (ORs) of treatment failure. RESULTS: In final analysis, 27 (7.5%) had treatment failure. Factors related to treatment failure including interim spacer exchange (OR, 3.13; confidence interval (CI), 1.04-9.09, p = 0.036), higher ESR level at reimplantation (OR, 1.85; CI, 1.05-3.57; p = 0.04), and time to reimplantation (OR, 1.00; CI, 1.003-1.005, p = 0.04). Performing revision arthroplasty surgery from 16 to 20 weeks had highest successful rate. The reimplantation over 24 weeks had a lower successful rate. However, no statistical significance in comparing each interval group. CONCLUSION: Our study emphasized the importance of timely reimplantation in achieving successful outcomes. Factors such as ESR levels, spacer exchange, and the duration of time to reimplantation influenced the likelihood of treatment failure in two-stage exchange arthroplasty for hip and knee PJI.

High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.

Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.

Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.

Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation.

A procedure to detect and identify specific chemicals of potential inhalation toxicity concern in aerosols.

OBJECTIVE: Understanding the potential inhalation toxicity of poorly characterized aerosols is challenging both because aerosols may contain numerous chemicals and because it is difficult to predict which chemicals may present significant inhalation toxicity concerns at the observed levels. We have developed a novel systematic procedure to address these challenges through non-targeted chemical analysis by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) and assessment of the results using publicly available toxicity data to prioritize the tentatively identified detected chemicals according to potential inhalation toxicity. MATERIALS AND METHODS: The procedure involves non-targeted chemical analysis of aerosol samples utilizing GC × GC-TOFMS, which is selected because it is an effective technique for detecting chemicals in complex samples and assigning tentative identities according to the mass spectra. For data evaluation, existing toxicity data (e.g. from the U.S. Environmental Protection Agency CompTox Chemicals Dashboard) are used to calculate multiple toxicity metrics that can be compared among the tentatively identified chemicals. These metrics include hazard quotient, incremental lifetime cancer risk, and metrics analogous to hazard quotient that we designated as exposure-(toxicology endpoint) ratios. RESULTS AND DISCUSSION: We demonstrated the utility of our procedure by detecting, identifying, and prioritizing specific chemicals of potential inhalation toxicity concern in the mainstream smoke generated from the machine-smoking of marijuana blunts. CONCLUSION: By designing a systematic approach for detecting and identifying numerous chemicals in complex aerosol samples and prioritizing the chemicals in relation to different inhalation toxicology endpoints, we have developed an effective approach to elucidate the potential inhalation toxicity of aerosols.

Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies.

The CD4 binding site (CD4bs) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies (bnAbs) that are attractive to elicit with vaccines. The CH235 lineage (VH1-46) of CD4bs bnAbs is particularly attractive because the most mature members neutralize 90% of circulating strains, do not possess long HCDR3 regions, and do not contain insertions and deletions that may be difficult to induce. We used virus neutralization to measure the interaction of CH235 unmutated common ancestor (CH235 UCA) with functional Env trimers on infectious virions to guide immunogen design for this bnAb lineage. Two Env mutations were identified, one in loop D (N279K) and another in V5 (G458Y), that acted synergistically to render autologous CH505 transmitted/founder virus susceptible to neutralization by CH235 UCA. Man5-enriched N-glycans provided additional synergy for neutralization. CH235 UCA bound with nanomolar affinity to corresponding soluble native-like Env trimers as candidate immunogens. A cryo-EM structure of CH235 UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 revealed interactions of the antibody light chain complementarity determining region 3 (CDR L3) with the engineered Env loops D and V5. These results demonstrate that virus neutralization can directly inform vaccine design and suggest a germline targeting and reverse engineering strategy to initiate and mature the CH235 bnAb lineage.

Correction: Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies.

[This corrects the article DOI: 10.1371/journal.ppat.1008026.].

Laparoscopic partial nephrectomy without intracorporeal suturing.

BACKGROUND: Partial nephrectomy has gained wider acceptance as a surgical technique in treating small renal tumors. Laparoscopic partial nephrectomy (LPN) still remains a technically demanding surgery to this day. We present our technique of laparoscopic partial nephrectomy, one that is performed without intracorporeal suturing. METHODS: We performed LPN on 31 patients with localized renal parenchymal tumor (stage T1). The procedures were done from September 2009 to March 2015 at the Kaohsiung Medical University Hospital and the Kaohsiung Municipal Ta-Tung Hospital. Our technique involves the covering of renal defect layer by layer with FloSeal, Tisseel and a fat pad after monopolar coagulation. RESULTS: Thirty-one patients were included in this study. Mean patient age was 53 years old (range 39-70). Mean tumor size was 2.9 cm (range 1.8-6.3). Mean RENAL nephrometry score was 5.3 (range 4-7). The average operation time was 188 min (range 120-290), and the average warm ischemic time was 19.0 min (range 9-26). Mean estimated blood loss was 171 ml (range 10-650), with no postoperative bleeding among the total 31 patients. No recurrent tumors were identified at a mean follow-up of 29 months postoperatively. The mean change in eGFR was 6.5 (ml/min/m2). CONCLUSION: Laparoscopic partial nephrectomy is a feasible surgical method for most patients with stage 1 tumor. Our technique has shown to reduce warm ischemic time significantly and provide patients with excellent functional outcomes without affecting oncological results. With this technique, surgeons can perform LPN with more efficiency and with fewer complications.

Graphene-Based Thermopile for Thermal Imaging Applications.

In this work, we leverage graphene's unique tunable Seebeck coefficient for the demonstration of a graphene-based thermal imaging system. By integrating graphene based photothermo-electric detectors with micromachined silicon nitride membranes, we are able to achieve room temperature responsivities on the order of ~7-9 V/W (at λ = 10.6 µm), with a time constant of ~23 ms. The large responsivities, due to the combination of thermal isolation and broadband infrared absorption from the underlying SiN membrane, have enabled detection as well as stand-off imaging of an incoherent blackbody target (300-500 K). By comparing the fundamental achievable performance of these graphene-based thermopiles with standard thermocouple materials, we extrapolate that graphene's high carrier mobility can enable improved performances with respect to two main figures of merit for infrared detectors: detectivity (>8 × 10(8) cm Hz(1/2) W(-1)) and noise equivalent temperature difference (<100 mK). Furthermore, even average graphene carrier mobility (<1000 cm(2) V(-1) s(-1)) is still sufficient to detect the emitted thermal radiation from a human target.

Dielectric screening of excitons and trions in single-layer MoS2.

Photoluminescence (PL) properties of single-layer MoS2 are indicated to have strong correlations with the surrounding dielectric environment. Blue shifts of up to 40 meV of exciton or trion PL peaks were observed as a function of the dielectric constant of the environment. These results can be explained by the dielectric screening effect of the Coulomb potential; based on this, a scaling relationship was developed with the extracted electronic band gap and exciton and trion binding energies in good agreement with theoretical estimations. It was also observed that the trion/exciton intensity ratio can be tuned by at least 1 order of magnitude with different dielectric environments. Our findings are helpful to better understand the tightly bound exciton properties in strongly quantum-confined systems and provide a simple approach to the selective and separate generation of excitons or trions with potential applications in excitonic interconnects and valleytronics.

Photoresponse of an electrically tunable ambipolar graphene infrared thermocouple.

We explore the photoresponse of an ambipolar graphene infrared thermocouple at photon energies close to or below monolayer graphene's optical phonon energy and electrostatically accessible Fermi energy levels. The ambipolar graphene infrared thermocouple consists of monolayer graphene supported by an infrared absorbing material, controlled by two independent electrostatic gates embedded below the absorber. Using a scanning infrared laser microscope, we characterize these devices as a function of carrier type and carrier density difference controlled at the junction between the two electrostatic gates. On the basis of these measurements, conducted at both mid- and near-infrared wavelengths, the primary detection mechanism can be modeled as a thermoelectric response. By studying the effect of different infrared absorbers, we determine that the optical absorption and thermal conduction of the substrate play the dominant role in the measured photoresponse of our devices. These experiments indicate a path toward hybrid graphene thermal detectors for sensing applications such as thermography and chemical spectroscopy.

Iron (III) chloride doping of CVD graphene.

Chemical doping has been shown as an effective method of reducing the sheet resistance of graphene. We present the results of our investigations into doping large area chemical vapor deposition graphene using Iron (III) Chloride (FeCl(3)). It is shown that evaporating FeCl(3) can increase the carrier concentration of monolayer graphene to greater than 10(14) cm(-2) and achieve resistances as low as 72 Ω sq(-1). We also evaluate other important properties of the doped graphene such as surface cleanliness, air stability, and solvent stability. Furthermore, we compare FeCl(3) to three other common dopants: Gold (III) Chloride (AuCl(3)), Nitric Acid (HNO(3)), and TFSA ((CF(3)SO(2))(2)NH). We show that compared to these dopants, FeCl(3) can not only achieve better sheet resistance but also has other key advantages including better solvent stability.

Synthesis of patched or stacked graphene and hBN flakes: a route to hybrid structure discovery.

Two-dimensional (2D) materials such as graphene and hexagonal boron nitride (hBN) have attracted significant attention due to their remarkable properties. Numerous interesting graphene/hBN hybrid structures have been proposed but their implementation has been very limited. In this work, the synthesis of patched structures through consecutive chemical vapor deposition (CVD) on the same substrate was investigated. Both in-plane junctions and stacked layers were obtained. For stacked layers, depending on the synthesis sequence, in one case turbostratic stacking with random rotations were obtained. In another, "AA-like", slightly twisted stacking between graphene and hBN was observed with lattice orientation misalignment consistently to be <1°. Raman characterizations not only confirmed that hBN is a superior substrate but also revealed for the first time that a graphene edge with hBN passivation displays reduced D band intensity compared to an open edge. These studies pave the way for the proposed well-ordered graphene/hBN structures and outline exciting future directions for hybrid 2D materials.

Rapid identification of stacking orientation in isotopically labeled chemical-vapor grown bilayer graphene by Raman spectroscopy.

The growth of large-area bilayer graphene has been of technological importance for graphene electronics. The successful application of graphene bilayers critically relies on the precise control of the stacking orientation, which determines both electronic and vibrational properties of the bilayer system. Toward this goal, an effective characterization method is critically needed to allow researchers to easily distinguish the bilayer stacking orientation (i.e., AB stacked or turbostratic). In this work, we developed such a method to provide facile identification of the stacking orientation by isotope labeling. Raman spectroscopy of these isotopically labeled bilayer samples shows a clear signature associated with AB stacking between layers, enabling rapid differentiation between turbostratic and AB-stacked bilayer regions. Using this method, we were able to characterize the stacking orientation in bilayer graphene grown through Low Pressure Chemical Vapor Deposition (LPCVD) with enclosed Cu foils, achieving almost 70% AB-stacked bilayer graphene. Furthermore, by combining surface sensitive fluorination with such hybrid (12)C/(13)C bilayer samples, we are able to identify that the second layer grows underneath the first-grown layer, which is similar to a recently reported observation.

The effect of copper pre-cleaning on graphene synthesis.

Copper foil is the most common substrate to synthesize monolayer graphene by chemical vapor deposition (CVD). The surface morphology and conditions of the copper foil can be very different depending on the various suppliers or different batches. These surface properties of copper strongly affect the growth behavior of graphene, thus rendering the growth conditions irreproducible when different batches of Cu foil are used. Furthermore, the quality of the graphene is severely affected as well. In this work, we report a facile method of copper pre-cleaning to improve the graphene quality and the reproducibility of the growth process. We found that the commercial Ni etchant (based on nitric acid) or nitric acid is the most effective cleaning agent among various acidic or basic solutions. The graphene grown on thus-treated copper surfaces is very clean and mostly monolayer when observed under scanning electron microscopy (SEM) and optical imaging, as compared to the graphene grown on untreated copper foil. Different batches (but with the same catalog number) of copper foil from Alfa Aesar Company were examined to explore the effect of copper pre-cleaning; consistent growth results were obtained when pre-cleaning was used. This method overcomes a commonly encountered problem in graphene growth and could become one of the standard protocols for preparing the copper foil substrate for growing graphene or other 2D materials.